We are running WP Multisite on 3.6.1 and haven't had a problem until yesterday afternoon. We are doing sub-domain for our multisite.
Now, when we upload the files for *one* of our multisite installations (the primary domain), it puts the files in the <doc_root>/files directory rather than <doc_root>/wp-content/blogs.dir/2/files folder. The exact same image gets put into the correct blogs.dir folder for the rest of the domains, so it is one blog out of seventeen that have this problem.
Before I go through the process of turning off/on plugins, can anyone think of why this might be the case? If it was more than one blog, I'd look at the .htaccess file, etc.
P.S. We've made blog with ID #2 the primary domain now, rather than #1. That was done yesterday afternoon, so it might be related.